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How-to populate MSI database with spectrum details

Before exporting a given UserContext to PRIDE XML file, check if the MSI database need to be populated with spectrum details.

:!: Since hEIDI 1.11.1, this functionality is no more available from the hEIDI GUI, but has to be executed (outside from hEIDI, see bellow) [by your system administrator].

Import spectrum using tool outside hEIDI [by your system administrator]

To import spectrum detail for a specified context using Paloma tool, you need to have the context id. This property is accessible in Context property sheet. View in accessproperties page.

  • Download Paloma-<version>.zip and unzip to <Paloma-install> directory. (Download is available at the following FTP site :
  • In command prompt (Run → Cmd), go to <Paloma-install>/ and run :
    java -Djava.library.path=./lib -Xms512m  -Xmx1024m  -classpath ./paloma-<version>.jar cea.edyp.palomae1.MainSpectrumFeeder [OPTIONS]
    • -Xmx option allow you to specify amount of memory to use for yhios process. Depending on your system (amount of memory and 32bits or 64bits), you can set more memory : -Xmx4000m for example
    • OPTIONS are described if no parameter is specified in command line… Nevertheless, here they are : -u <user> -p <password> -url <dbURL> -m <root> [-d <driver>] -cid <context_id> where
      • <user> : user for DB connection
      • <password> : password for DB connection
      • <dbURL> : url to DB such as jdbc:postgresql:/ / <server_name>/<DB_Name>
      • <root> : Path to mascot data files
      • <driver> : Optional, default is Postgresql driver (org.postgresql.Driver)
      • <context_id> : Context ID to get spectra for
  • You can verify there were no error by opening paloma-<user>.log from <Paloma-install> directory. This file contains lots of information, for debug purpose.
    • Search for any “ERROR ” string to verify no error occurs.
    • You can also see how many mascot dat file were parsed.

Look for entry such has

         INFO SpectrumEntriesSearch - The selected context contains 2,686 species and 2,686 spectrum are needed
         INFO SpectrumEntriesSearch - Paloma - SpectrumEntriesSearch - identify 44 dat files
         INFO SpectrumEntriesSearch -  .... featuring 2686 peptides
         INFO SpectrumMatchFeeder - Paloma - SpectrumMatchFeeder - will parse 44 dat files 
  • You will also see “44” entry like Parser dat file : XXXXX. Each followed by Parser dat file DONE

Import spectrum using hEIDI

:!: Since hEIDI 1.11.1, this functionality is no more available. Should be reintegrated …

  • After having created or opened an hEIDI project, open your MSI session but :!: Don't forget to activate your hEIDI project.
  • Check, in Windows Explorer, you have mapped a drive to the Mascot data folder (\\cp-mascot\data) and you are connected to that folder.
  • Select a UserContext. It has to be grouped and saved to MSIdb.
  • Select the menu MS Identifications→Database Update→Populate with spectra
  • A dialog will appear on the screen to indicate if spectrum details are missing for this UserContext
  • Check the Mascot data root path. You can use \\cp-mascot\data or the corresponding Drive Letter you have set up in Windows Explorer, for example Y:.

  • If spectrum details are missing, click on Ok, populate MSIdb with missing spectra, else click on Do nothing & Close this window
  • In case you have clicked Yes, a message will appear when process is finished

how_to/spectrummatchfeeder.txt · Last modified: 2013/04/11 10:41 by